I have a miss from 4000 rpm to WOT. The boat was just picked up at a local shop where they replaced the upper coil, but same problem. Could low battery voltage cause the problem? It seems to occur after fishing all day while running trolling motor and bait tank.
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It does sound like an electrical issue. Having the problem after running the battery down makes sense as the charging components are forced to work harder and get hotter. Hot temps is not good for electrical components because the insulation degrades. Often the problem will only be noticeable when the engine is hot becaused of thermal growth and degradation of winding insulation causing intermittent shorts. The stator under the flywheel has both winding for the charging circuit and for the ignition (both low and high speed) windings. Possibly one of the high speed coils. Sometimes a bad regulator can cause a miss. It is not uncommon for a John/Rude stator to fail because the OEM stators are potted (sealed in resin) which does not let them cool properly. Aftermarket stator are not potted for this reason. My 2011 90 ETEC stator is not potted so it looks like Evinrude (maybe because of BRP) got smart.
BRP no uses CDI for replacement parts, so if you buy OEM, you;ll get CDI, its good stuff, but its cheaper to buy the CDI from a distributor than go thru BRP